If you see a box that is highlighted yellow in the grader report, this means that the grade has been manually overridden. When a grade is overridden in this way, then any other grade earned (for instance, by taking a quiz, or from being graded in an assignment rubric) will not display.
To remove an overridden grade, you must first turn editing on in the grader report, then click the gear icon next to the grade in question. On the next screen, you'll see a checkbox labelled "Overridden". Simply uncheck the box and save your changes, then any other grade the student earned will display in the grade reports.